Add some tests for the nlme convenience functions

6 files changed, 89 insertions, 15 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 1aa5cac2..a9d0e939 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.49.9
-Date: 2020-03-31
+Version: 0.9.49.10
+Date: 2020-04-07
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de",
                     comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/build.log b/build.log
index b0765ebb..af1a7be5 100644
--- a/build.log
+++ b/build.log
@@ -6,5 +6,5 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 * looking to see if a ‘data/datalist’ file should be added
-* building ‘mkin_0.9.49.9.tar.gz’
+* building ‘mkin_0.9.49.10.tar.gz’
 
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 4bf07370..99895400 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -32,8 +32,9 @@ for parallel execution.}
 \item{\dots}{Further arguments that will be passed to \code{\link{mkinfit}}.}
 }
 \value{
-A matrix of \code{\link{mkinfit}} objects that can be indexed using
-  the model and dataset names as row and column indices.
+A two-dimensional \code{\link{array}} of \code{\link{mkinfit}}
+  objects that can be indexed using the model names for the first index (row index) 
+  and the dataset names for the second index (column index).
 }
 \description{
 This function calls \code{\link{mkinfit}} on all combinations of models and
diff --git a/test.log b/test.log
index 84b13a10..877d5193 100644
--- a/test.log
+++ b/test.log
@@ -6,15 +6,25 @@ Testing mkin
 ✔ |   4       | Calculation of FOCUS chi2 error levels [2.2 s]
 ✔ |   4       | Fitting the SFORB model [1.7 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [9.6 s]
-✔ |  14       | Error model fitting [38.4 s]
-✔ |   6       | Test fitting the decline of metabolites from their maximum [0.7 s]
+✔ |  10       | Confidence intervals and p-values [9.4 s]
+✔ |  14       | Error model fitting [37.5 s]
+✔ |   6       | Test fitting the decline of metabolites from their maximum [0.8 s]
 ✔ |   1       | Fitting the logistic model [0.9 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
-✔ |  12       | Special cases of mkinfit calls [2.2 s]
+✔ |  12       | Special cases of mkinfit calls [2.3 s]
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.3 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.2 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
+✖ |   0 1     | Nonlinear mixed-effects models [1.3 s]
+────────────────────────────────────────────────────────────────────────────────
+test_nlme.R:37: error: nlme_function works correctly
+konnte Funktion "nlme_f" nicht finden
+Backtrace:
+ 1. nlme::nlme(...) tests/testthat/test_nlme.R:37:2
+ 2. nlme::nlme.formula(...)
+ 3. [ base::eval(...) ] with 1 more call
+ 5. [ base::eval(...) ] with 1 more call
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
 ✔ |   3       | Summary
 ✔ |  11       | Plotting [0.6 s]
@@ -22,17 +32,17 @@ Testing mkin
 ✔ |   2       | Residuals extracted from mkinfit models
 ✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
-✔ |   7     1 | Hypothesis tests [32.5 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s]
+✔ |   7     1 | Hypothesis tests [31.9 s]
 ────────────────────────────────────────────────────────────────────────────────
 test_tests.R:60: skip: We can do a likelihood ratio test using an update specification
 Reason: This errors out if called by testthat while it works in a normal R session
 ────────────────────────────────────────────────────────────────────────────────
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 112.1 s
+Duration: 111.4 s
 
 OK:       138
-Failed:   0
+Failed:   1
 Warnings: 0
 Skipped:  1
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index fe5e481a..f492a57f 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-04-01
+Date: 2020-04-07
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
new file mode 100644
index 00000000..b3c41f00
--- /dev/null
+++ b/tests/testthat/test_nlme.R
@@ -0,0 +1,63 @@
+context("Nonlinear mixed-effects models")
+
+test_that("nlme_function works correctly", {
+
+  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+  m_SFO <- mkinmod(parent = mkinsub("SFO"))
+  d_SFO_1 <- mkinpredict(m_SFO,
+    c(k_parent_sink = 0.1),
+    c(parent = 98), sampling_times)
+  d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
+  d_SFO_2 <- mkinpredict(m_SFO,
+    c(k_parent_sink = 0.05),
+    c(parent = 102), sampling_times)
+  d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
+  d_SFO_3 <- mkinpredict(m_SFO,
+    c(k_parent_sink = 0.02),
+    c(parent = 103), sampling_times)
+  d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
+
+  d1 <- add_err(d_SFO_1, function(value) 3, n = 1, seed = 123456)
+  d2 <- add_err(d_SFO_2, function(value) 2, n = 1, seed = 234567)
+  d3 <- add_err(d_SFO_3, function(value) 4, n = 1, seed = 345678)
+  ds <- c(d1 = d1, d2 = d2, d3 = d3)
+
+  f <- mmkin("SFO", ds, cores = 1, quiet = TRUE)
+
+  mean_dp <- mean_degparms(f)
+  grouped_data <- nlme_data(f)
+  nlme_f <- nlme_function(f)
+
+  m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
+    data = grouped_data,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = mean_dp)
+
+  m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
+    data = grouped_data,
+    fixed = parent_0 + log_k_parent_sink ~ 1,
+    random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+    start = mean_dp)
+
+  expect_equal(m_nlme_raw$coefficients, m_nlme_mkin$coefficients)
+
+  m_nlme_raw_up_1 <- update(m_nlme_raw, random = log_k_parent_sink ~ 1)
+  # The following two calls give an error although they should
+  # do the same as the call above
+  # The error occurs in the evaluation of the modelExpression in the
+  # call to .C(fit_nlme, ...)
+  # m_nlme_mkin_up_1 <- update(m_nlme_mkin, random = log_k_parent_sink ~ 1)
+  # m_nlme_mkin <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
+  #   data = grouped_data,
+  #   fixed = parent_0 + log_k_parent_sink ~ 1,
+  #   random = log_k_parent_sink ~ 1,
+  #   start = mean_dp)
+
+  m_nlme_raw_up_2 <- update(m_nlme_raw, random = parent_0 ~ 1)
+  m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1)
+  expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients)
+
+  # update(m_nlme_mkin) # works
+
+})